If the ship is in the atmosphere or in space and you are in a ship that has room for at least one more person(ex. a freighter) in the same square, make yourself Commander and Pilot, go to the entrance and there should be an option to board the ship outside and to kick the passenger. When you kick the passenger, he/she will go aboard the freighter. The point is, there has to be somewhere for the passenger to go safely if you are in space. This worked for me.